Article
Physics, Fluids & Plasmas
G. A. Patterson
Summary: This paper experimentally studies the dynamics of a self-propelled stochastic particle under the influence of an axisymmetric light field. The study reveals the existence of bistability in the orbital trajectories and introduces a mathematical model to explain the experimental observations. It is found that the location of the sensor can induce trapped or diffusive behaviors, contributing to the bistability in the orbital trajectories.
Article
Biochemical Research Methods
Mark Jayson Cortez, Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim, Kresimir Josic
Summary: This study proposes a non-Markovian, hierarchical Bayesian inference framework for quantifying the variability of cellular processes within and across cells in a population. By using a delayed birth-death process, the proposed hierarchical framework is shown to be robust and leads to improved estimates compared to its non-hierarchical counterpart when applied to in silico and experimental data. The mean delays in protein production are reported to be larger than previously thought, with a coefficient of variation of around 0.2 across the population, and not strongly correlated with protein production or growth rates.
Article
Cell Biology
Martijn Wehrens, Laurens H. J. Krah, Benjamin D. Towbin, Rutger Hermsen, Sander J. Tans
Summary: This study reveals that catabolic enzyme expression in E. coli cells continuously responds to metabolic fluctuations, which is regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system. The study uses single-cell microscopy, genetic constructs, and mathematical modeling to show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. The findings suggest that the cAMP-CRP system may have evolved to control both internal metabolic fluctuations and external growth conditions.
Article
Multidisciplinary Sciences
Jin-Xiu Li, Xue-Zhen Huang, Wei-ping Fu, Xiao-hua Zhang, David H. Mauki, Jing Zhang, Chang Sun, Lu-Ming Dai, Li Zhong, Li Yu, Ya-ping Zhang
Summary: This study conducted comprehensive bioinformatics analyses and experimental verifications to explore the regulatory mechanism of rs10516526 and GSTCD in COPD. The results showed that low expression of GSTCD was associated with COPD, and the transcription factors C-Jun and CREB1 were found to be essential for the regulation of GSTCD by specific genetic signals. Moreover, certain mutated forms of these signals showed a stronger binding ability to the transcription factors, potentially leading to allele-specific regulation and reduced susceptibility to COPD.
Article
Medicine, Research & Experimental
Isabel Mayoral-Gonzalez, Eva M. Calderon-Sanchez, Isabel Galeano-Otero, Marta Martin-Bornez, Encarnacion Gutierrez-Carretero, Maria Fernandez-Velasco, Nieves Domenech, Maria Generosa Crespo-Leiro, Ana Maria Gomez, Antonio Ordonez-Fernandez, Abdelkrim Hmadcha, Tarik Smani
Summary: Ucn-2 has been found to exert cardioprotective effects through the regulation of miR-29a, reducing fibrosis and apoptosis caused by myocardial I/R injury. Furthermore, elevated expression of Hmox-1 in the ventricle of ischemic patients with heart failure was observed, which was inversely correlated with left ventricle ejection fraction.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Review
Genetics & Heredity
Abhishek Sarkar, Matthew Stephens
Summary: The Perspective suggests that a Poisson measurement model is sufficient for analyzing single-cell RNA sequencing data and could resolve current controversies. It argues against inconsistent terminology such as dropout and missing data. The development of methods should start with a simple Poisson model, as it is generally consistent with existing data.
Article
Biochemical Research Methods
Asia Mendelevich, Saumya Gupta, Aleksei Pakharev, Athanasios Teodosiadis, Andrey A. Mironov, Alexander A. Gimelbrant
Summary: A new spike-in approach is developed to correct technical noise in allele-specific expression analysis, which is highly accurate and cost-effective. This approach involves adding a distinct RNA as a spike-in before library preparation, allowing for efficient analysis of allele-specific expression in large studies.
Article
Optics
Jiangshuoxue Han, Yang Liu, Zejiang Deng, Gehui Xie, Daping Luo, Chenglin Gu, Lian Zhou, Wenxue Li
Summary: This study measured gain-parameter-dependent transfer functions and phase-noise performances in a mode-locked Yb-doped fiber laser. It was found that the corner frequency in the amplitude and phase domains is determined by the absorption coefficient of the gain fiber, with higher dopant concentration resulting in more phase noise accumulation. Additionally, net cavity dispersion-dependent transfer functions were presented to verify the effect of dispersion management on the frequency response, deriving a guideline for optimizing mode-locked fiber laser design to achieve low phase noise and timing jitter.
HIGH POWER LASER SCIENCE AND ENGINEERING
(2021)
Article
Biology
Juil Kim, Yuseok Moon
Summary: Kim and Moon discovered that the transcription factor PRDM1 is upregulated in colorectal cancer (CRC) cells in response to ribosomal dysfunction, leading to chemoresistance through the IGF signaling pathway. They also found that PRDM1 promotes cancer cell stemness and survival, providing insights into environmental stress-mediated signaling in CRC.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Henriette Lyng Roder, Urvish Trivedi, Jakob Russel, Kasper Norskov Kragh, Jakob Herschend, Ida Thalso-Madsen, Tim Tolker-Nielsen, Thomas Bjarnsholt, Mette Burmolle, Jonas Stenlokke Madsen
Summary: Plasmids can be stored in biofilms, allowing them to persist even under non-selective conditions. However, under these conditions, cells carrying plasmids may promote the dispersal of cells without plasmids, turning biofilms into plasmid sinks.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Review
Cell Biology
Isabel Pereira-Castro, Alexandra Moreira
Summary: Selective polyadenylation (APA) fine-tunes gene expression and controls mRNA fate and function in different cellular states. Different lengths of 3'-UTRs are associated with specific cellular states and diseases, with short 3'-UTRs linked to proliferative and cancer cells, and long 3'-UTRs mainly found in polarized and differentiated cells.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Biochemistry & Molecular Biology
Marika Linsky, Gil Segal
Summary: The study identified a novel genomic island in L. pneumophila, encoding two Icm/Dot effectors and a LuxR type regulator. It was found that RegK3 directly activates the expression levels of legK3 and cegK3 effector-encoding genes, while Fis repressors silence the expression of all components in the island. The expression profiles of these genes varied among different Legionella species, with RegK3 activation levels correlated with Fis-mediated repression, suggesting potential co-regulation and functional synergy between LegK3 and CegK3 effectors.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biology
Lucy Ham, Marcel Jackson, Michael P. H. Stumpf
Summary: Single-cell expression profiling reveals extensive cell-to-cell variability at the transcriptomic and proteomic level, posing challenges in inferring dynamics and causes of variability. New mathematical models and experimental set-ups are proposed to distinguish intrinsic and extrinsic noise, providing insights into understanding the origins and effects of cell-to-cell variability.
Article
Biochemical Research Methods
Joshua J. R. Burns, Benjamin T. Shealy, Mitchell S. Greer, John A. Hadish, Matthew T. McGowan, Tyler Biggs, Melissa C. Smith, F. Alex Feltus, Stephen P. Ficklin
Summary: Gene co-expression networks (GCNs) provide benefits to molecular research, but large multivariable datasets pose challenges to their construction. The use of a knowledge independent network construction toolkit can address these challenges and result in context-specific GCNs (csGCNs).
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Engineering, Multidisciplinary
Song Yi, Xu Wei, Niu LiZhi
Summary: Gene expression is inherently noisy and affected by random fluctuations. This study considers the transition dynamics in a gene regulatory system and finds that increasing the initial concentration can improve transcription. The results indicate that larger jumps in noise and smaller noise intensity can shorten the time for state transition and boost protein production.
SCIENCE CHINA-TECHNOLOGICAL SCIENCES
(2022)
Correction
Biochemistry & Molecular Biology
Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Joshua Gould, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, Eric S. Lander
Article
Biochemistry & Molecular Biology
Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Joshua Gould, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, Eric S. Lander
Article
Biochemistry & Molecular Biology
Ninib Baryawno, Dariusz Przybylski, Monika S. Kowalczyk, Youmna Kfoury, Nicolas Severe, Karin Gustafsson, Konstantinos D. Kokkaliaris, Francois Mercier, Marcin Tabaka, Matan Hofree, Danielle Dionne, Ani Papazian, Dongjun Lee, Orr Ashenberg, Ayshwarya Subramanian, Eeshit Dhaval Vaishnav, Orit Rozenblatt-Rosen, Aviv Regev, David T. Scadden
Article
Immunology
Heping Xu, Jiarui Ding, Caroline B. M. Porter, Antonia Wallrapp, Marcin Tabaka, Sai Ma, Shujie Fu, Xuanxuan Guo, Samantha J. Riesenfeld, Chienwen Su, Danielle Dionne, Lan T. Nguyen, Ariel Lefkovith, Orr Ashenberg, Patrick R. Burkett, Hai Ning Shi, Orit Rozenblatt-Rosen, Daniel B. Graham, Vijay K. Kuchroo, Aviv Regev, Ramnik J. Xavier
Article
Immunology
Marieke Lavaert, Kai Ling Liang, Niels Vandamme, Jong-Eun Park, Juliette Roels, Monica S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Bart Vandekerckhove, Georges Leclercq, Aviv Regev, Pieter Van Vlierberghe, Martin Guilliams, Sarah A. Teichmann, Yvan Saeys, Tom Taghon
Article
Biochemical Research Methods
Bo Li, Joshua Gould, Yiming Yang, Siranush Sarkizova, Marcin Tabaka, Orr Ashenberg, Yanay Rosen, Michal Slyper, Monika S. Kowalczyk, Alexandra-Chloe Villani, Timothy Tickle, Nir Hacohen, Orit Rozenblatt-Rosen, Aviv Regev
Article
Multidisciplinary Sciences
Jakub Jedrak, Anna Ochab-Marcinek
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Erik L. Bao, Satish K. Nandakumar, Xiaotian Liao, Alexander G. Bick, Juha Karjalainen, Marcin Tabaka, Olga Gan, Aki S. Havulinna, Tuomo T. J. Kiiskinen, Caleb A. Lareau, Aitzkoa L. de Lapuente Portilla, Bo Li, Connor Emdin, Veryan Codd, Christopher P. Nelson, Christopher J. Walker, Claire Churchhouse, Albert de la Chapelle, Daryl E. Klein, Bjorn Nilsson, Peter W. F. Wilson, Kelly Cho, Saiju Pyarajan, J. Michael Gaziano, Nilesh J. Samani, Aviv Regev, Aarno Palotie, Benjamin M. Neale, John E. Dick, Pradeep Natarajan, Christopher J. O'Donnell, Mark J. Daly, Michael Milyavsky, Sekar Kathiresan, Vijay G. Sankaran
Article
Multidisciplinary Sciences
Karen O. Dixon, Marcin Tabaka, Markus A. Schramm, Sheng Xiao, Ruihan Tang, Danielle Dionne, Ana. C. Anderson, Orit Rozenblatt-Rosen, Aviv Regev, Vijay K. Kuchroo
Summary: Research demonstrates the crucial role of TIM-3 in regulating dendritic cell (DC) function, with TIM-3 deletion promoting strong anti-tumour immunity by preventing DCs from expressing a regulatory program and facilitating the maintenance of CD8(+) effector and stem-like T cells. The absence of TIM-3 in DCs leads to increased accumulation of reactive oxygen species, resulting in NLRP3 inflammasome activation, and inhibition of inflammasome activation or downstream effector cytokines IL-1 beta and IL-18 abrogates the protective anti-tumour immunity observed with TIM-3 deletion in DCs.
Article
Multidisciplinary Sciences
Yaara Oren, Michael Tsabar, Michael S. Cuoco, Liat Amir-Zilberstein, Heidie F. Cabanos, Jan-Christian Hutter, Bomiao Hu, Pratiksha I. Thakore, Marcin Tabaka, Charles P. Fulco, William Colgan, Brandon M. Cuevas, Sara A. Hurvitz, Dennis J. Slamon, Amy Deik, Kerry A. Pierce, Clary Clish, Aaron N. Hata, Elma Zaganjor, Galit Lahav, Katerina Politi, Joan S. Brugge, Aviv Regev
Summary: Recent studies have revealed that cancer cells can enter different lineages in response to treatment, with distinct biological characteristics and metabolic programs. Proliferative capacity of drug-tolerant persister cells is associated with upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation.
Article
Multidisciplinary Sciences
Laura Jardine, Simone Webb, Issac Goh, Mariana Quiroga Londono, Gary Reynolds, Michael Mather, Bayanne Olabi, Emily Stephenson, Rachel A. Botting, Dave Horsfall, Justin Engelbert, Daniel Maunder, Nicole Mende, Caitlin Murnane, Emma Dann, Jim McGrath, Hamish King, Iwo Kucinski, Rachel Queen, Christopher D. Carey, Caroline Shrubsole, Elizabeth Poyner, Meghan Acres, Claire Jones, Thomas Ness, Rowen Coulthard, Natalina Elliott, Sorcha O'Byrne, Myriam L. R. Haltalli, John E. Lawrence, Steven Lisgo, Petra Balogh, Kerstin B. Meyer, Elena Prigmore, Kirsty Ambridge, Mika Sarkin Jain, Mirjana Efremova, Keir Pickard, Thomas Creasey, Jaume Bacardit, Deborah Henderson, Jonathan Coxhead, Andrew Filby, Rafiqul Hussain, David Dixon, David McDonald, Dorin-Mirel Popescu, Monika S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Aviv Regev, Sam Behjati, Elisa Laurenti, Nicola K. Wilson, Anindita Roy, Berthold Goettgens, Irene Roberts, Sarah A. Teichmann, Muzlifah Haniffa
Summary: Research demonstrates that the full blood and immune cell repertoire in fetal bone marrow is established within a short 6-7 week period in early second trimester, promoting rapid and extensive diversification of myeloid cells, with distinct differences from fetal liver.
Article
Medicine, Research & Experimental
Dominik Lewandowski, Andrzej T. Foik, Roman Smidak, Elliot H. Choi, Jianye Zhang, Thanh Hoang, Aleksander Tworak, Susie Suh, Henri Leinonen, Zhiqian Dong, Antonio Fm Pinto, Emily Tom, Jennings Luu, Joan Lee, Xiuli Ma, Erhard Bieberich, Seth Blackshaw, Alan Saghatelian, David C. Lyon, Dorota Skowronska-Krawczyk, Marcin Tabaka, Krzysztof Palczewski
Summary: The absence of AdipoR1 in mice leads to progressive photoreceptor degeneration, reduced electroretinogram amplitudes, decreased retinoid content, and reduced cone opsin expression. Accumulation of ceramides in the AdipoR1(-/-) retina results in photoreceptor death. Treatment with desipramine/L-cycloserine lowers ceramide levels and protects photoreceptors in AdipoR1(-/-) mice. Prolonged treatment with these drugs improves cone-mediated retinal function and corrects the electrical responses of the primary visual cortex.
Article
Immunology
Ruihan Tang, Nandini Acharya, Ayshwarya Subramanian, Vinee Purohit, Marcin Tabaka, Yu Hou, Danyang He, Karen O. Dixon, Connor Lambden, Junrong Xia, Orit Rozenblatt-Rosen, Raymond A. Sobel, Chao Wang, Aviv Regev, Ana C. Anderson, Vijay K. Kuchroo
Summary: Dendritic cells (DCs) play a crucial role in modulating the immune response by sensing environmental cues. This study identifies Bat3 as an endogenous regulator of DC function, showing that loss of Bat3 expression alters the T cell compartment, resulting in the attenuation of autoimmunity and acceleration of tumor growth.
SCIENCE IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Joachim De Jonghe, Tomasz S. Kaminski, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka-Goetz, Sarah A. Teichmann, Florian Hollfelder
Summary: The authors developed spinDrop, a technique that increases gene detection and reduces noise in droplet microfluidics, to generate a high-quality molecular atlas of mouse brain development.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Fluids & Plasmas
Jakub Jedrak, Maciej Kwiatkowski, Anna Ochab-Marcinek